taxonomy download from NCBI based on geneID
0
0
Entering edit mode
Jitendra ▴ 10
@nabiyogesh-11718
Last seen 4 days ago
United Kingdom

Is it possible to download taxonomy based on gene Id for a large dataset from NCBI using biomartr package?

vi arsM.ID.txt

AAAK03000116.1
AAAL02000001.1
AACD01000079.1
AACS02000002.1
AADV02000002.1
AADV02000014.1
AADV02000142.1
AADV02000157.1
AADV02000160.1
AADV02000163.1
AAEK01000011.1
AAEK01000037.1
AAEW02000007.1
AAEW02000015.1
AAEW02000015.1

taxonomy format should be like below:

I need taxonomy in this format:

AM774418.1 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobacterium  Halobacterium salinarum R1
LOPV01000533.1 Archaea; Euryarchaeota; Halobacteria; Haloferacales; Haloferacaceae; Haloferax  Haloferax sp. SB29
CP003125.1      Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus; Geobacillus thermoleovorans group  Geobacillus 
BAWP01000033.1  Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Parageobacillus Parageobacillus thermoglucosidasius NBRC 
MEFJ01000016.1  Bacteria; Proteobacteria; Betaproteobacteria; Nitrosomonadales; Thiobacillaceae; Thiobacillus   Thiobacillus sp. SCN 
FXAE01000009.1  Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus      Paenibacillus barengoltzii J12
biomartr Bioconducter • 730 views
ADD COMMENT

Login before adding your answer.

Traffic: 1113 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6